[gmx-users] How to include FE2+ in ions.itp ?

[Justin A. Lemkul]

Tanos Franca wrote:
>     Dear GROMACS users,
>     We're trying to perform a MD simulation of a system with a hematin 
> group but realized that GROMACS does not have parameters for the ion 
> FE2+. We tried to include the parametrs in the file ions.itp but did not 
> suceed yet. Does anybody knows the right procedure to introduce this 

It would be helpful to know exactly where you're stuck, otherwise we're left 
guessing as to what you've tried.

> ions into the file ions.itp ? Do we have to change anything more in 
> order to GROMACS recognize the new ion ?

You may have to introduce a new atom type into the .atp file, and set nonbonded 
parameters for it in ffnonbonded.itp, but also be aware that a crude 
representation of a transition metal as a normal point charge may not be 
terribly accurate:

http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

Also, please do not send messages that copy the entire digest (or any unrelated 
content, for that matter).  It confuses the archive.

-Justin

>     With my best regards,
>     Tanos C. C. Franca.
>     Coordinator of the Graduate Program in Chemistry
>     Military Institute of Engineering.
>     Rio de Janeiro/RJ
>     Brazil.

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================